All Samsung smartphones including the latest Galaxy S4 include a “binary counter”. This counter only increases when you install non-official Samsung recovery. So if you end up installing ClockworkMod or TWRP recovery to install custom ROMs, this binary counter is increased.
If you do flash an official Samsung firmware (or root-injected Samsung firmware), the binary counter does not increase.
Fortunately, XDA developer ChainFire develops Triangle Away app which allows you to reset the binary counter.
What does this mean for you as a consumer?
Nothing, you can always get your Galaxy S4 completely back to stock by installing an official Samsung firmware and also resetting binary counter using Triangle Away app. The beauty of Samsung phones like Galaxy S4 is that it is possible to “unvoid” your warranty completely back to stock easily using free online tools unlikes HTC, where you can re-lock HTC phones but HTC will still know you’ve rooted your device.